reorganizing files

fredhutchio · Dec 9, 2020 · 15efb3e · 15efb3e
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diff --git a/exercises/README.md b/exercises/README.md
diff --git a/exercises/week1_exercises.txt b/exercises/week1_exercises.txt
diff --git a/exercises/week2_exercises.txt b/exercises/week2_exercises.txt
diff --git a/exercises/week3_exercises.txt b/exercises/week3_exercises.txt
diff --git a/exercises/week4_exercises.txt b/exercises/week4_exercises.txt
diff --git a/class2_figures/UMI_log.png → monocle/class2_figures/UMI_log.png b/class2_figures/UMI_log.png → monocle/class2_figures/UMI_log.png
diff --git a/class2_figures/UMI_standard.png → monocle/class2_figures/UMI_standard.png b/class2_figures/UMI_standard.png → monocle/class2_figures/UMI_standard.png
diff --git a/class2_figures/cds_umigood.png → monocle/class2_figures/cds_umigood.png b/class2_figures/cds_umigood.png → monocle/class2_figures/cds_umigood.png
diff --git a/class2_figures/cds_view1.png → monocle/class2_figures/cds_view1.png b/class2_figures/cds_view1.png → monocle/class2_figures/cds_view1.png
diff --git a/class2_figures/cds_view2.png → monocle/class2_figures/cds_view2.png b/class2_figures/cds_view2.png → monocle/class2_figures/cds_view2.png
diff --git a/class2_figures/colData_view.png → monocle/class2_figures/colData_view.png b/class2_figures/colData_view.png → monocle/class2_figures/colData_view.png
diff --git a/class2_figures/plot_pc_variance.png → monocle/class2_figures/plot_pc_variance.png b/class2_figures/plot_pc_variance.png → monocle/class2_figures/plot_pc_variance.png
diff --git a/class2_figures/readme → monocle/class2_figures/readme b/class2_figures/readme → monocle/class2_figures/readme
diff --git a/..._figures/umap_cluster_noresindication.png → ..._figures/umap_cluster_noresindication.png b/..._figures/umap_cluster_noresindication.png → ..._figures/umap_cluster_noresindication.png
diff --git a/class2_figures/umap_cluster_res.png → monocle/class2_figures/umap_cluster_res.png b/class2_figures/umap_cluster_res.png → monocle/class2_figures/umap_cluster_res.png
diff --git a/class2_figures/umap_nocluster.png → monocle/class2_figures/umap_nocluster.png b/class2_figures/umap_nocluster.png → monocle/class2_figures/umap_nocluster.png
diff --git a/class3_figures/auto_cell_type.png → monocle/class3_figures/auto_cell_type.png b/class3_figures/auto_cell_type.png → monocle/class3_figures/auto_cell_type.png
diff --git a/class3_figures/auto_ext_type.png → monocle/class3_figures/auto_ext_type.png b/class3_figures/auto_ext_type.png → monocle/class3_figures/auto_ext_type.png
diff --git a/class3_figures/heatmap_legend.png → monocle/class3_figures/heatmap_legend.png b/class3_figures/heatmap_legend.png → monocle/class3_figures/heatmap_legend.png
diff --git a/class3_figures/manual_cell_type.png → monocle/class3_figures/manual_cell_type.png b/class3_figures/manual_cell_type.png → monocle/class3_figures/manual_cell_type.png
diff --git a/class3_figures/manual_ext_type.png → monocle/class3_figures/manual_ext_type.png b/class3_figures/manual_ext_type.png → monocle/class3_figures/manual_ext_type.png
diff --git a/class3_figures/readme → monocle/class3_figures/readme b/class3_figures/readme → monocle/class3_figures/readme
diff --git a/class3_figures/scores.png → monocle/class3_figures/scores.png b/class3_figures/scores.png → monocle/class3_figures/scores.png
diff --git a/class4_figures/color_cells_by_pseudotime.png → ...ss4_figures/color_cells_by_pseudotime.png b/class4_figures/color_cells_by_pseudotime.png → ...ss4_figures/color_cells_by_pseudotime.png
diff --git a/class4_figures/gene_module_heatmap.png → ...le/class4_figures/gene_module_heatmap.png b/class4_figures/gene_module_heatmap.png → ...le/class4_figures/gene_module_heatmap.png
diff --git a/class4_figures/genes_of_interest.png → monocle/class4_figures/genes_of_interest.png b/class4_figures/genes_of_interest.png → monocle/class4_figures/genes_of_interest.png
diff --git a/class4_figures/head_agg_exp.png → monocle/class4_figures/head_agg_exp.png b/class4_figures/head_agg_exp.png → monocle/class4_figures/head_agg_exp.png
diff --git a/class4_figures/head_cell_group.png → monocle/class4_figures/head_cell_group.png b/class4_figures/head_cell_group.png → monocle/class4_figures/head_cell_group.png
diff --git a/class4_figures/head_diff_genes.png → monocle/class4_figures/head_diff_genes.png b/class4_figures/head_diff_genes.png → monocle/class4_figures/head_diff_genes.png
diff --git a/class4_figures/head_gene_modules.png → monocle/class4_figures/head_gene_modules.png b/class4_figures/head_gene_modules.png → monocle/class4_figures/head_gene_modules.png
diff --git a/class4_figures/learn_graph_plot.png → monocle/class4_figures/learn_graph_plot.png b/class4_figures/learn_graph_plot.png → monocle/class4_figures/learn_graph_plot.png
diff --git a/class4_figures/order_cells_selected_node.png → ...ss4_figures/order_cells_selected_node.png b/class4_figures/order_cells_selected_node.png → ...ss4_figures/order_cells_selected_node.png
diff --git a/class4_figures/order_cells_view.png → monocle/class4_figures/order_cells_view.png b/class4_figures/order_cells_view.png → monocle/class4_figures/order_cells_view.png
diff --git a/class4_figures/readme → monocle/class4_figures/readme b/class4_figures/readme → monocle/class4_figures/readme
diff --git a/class4_figures/reloaded_UMAP.png → monocle/class4_figures/reloaded_UMAP.png b/class4_figures/reloaded_UMAP.png → monocle/class4_figures/reloaded_UMAP.png
diff --git a/class4_figures/top5_specific_markers.png → .../class4_figures/top5_specific_markers.png b/class4_figures/top5_specific_markers.png → .../class4_figures/top5_specific_markers.png
diff --git a/lung_data/Lung-10X_P7_8/barcodes.tsv → monocle/lung_data/Lung-10X_P7_8/barcodes.tsv b/lung_data/Lung-10X_P7_8/barcodes.tsv → monocle/lung_data/Lung-10X_P7_8/barcodes.tsv
diff --git a/lung_data/Lung-10X_P7_8/cds_class1.RDS → ...le/lung_data/Lung-10X_P7_8/cds_class1.RDS b/lung_data/Lung-10X_P7_8/cds_class1.RDS → ...le/lung_data/Lung-10X_P7_8/cds_class1.RDS
diff --git a/lung_data/Lung-10X_P7_8/dense_matrix.txt.zip → ...g_data/Lung-10X_P7_8/dense_matrix.txt.zip b/lung_data/Lung-10X_P7_8/dense_matrix.txt.zip → ...g_data/Lung-10X_P7_8/dense_matrix.txt.zip
diff --git a/lung_data/Lung-10X_P7_8/genes.tsv → monocle/lung_data/Lung-10X_P7_8/genes.tsv b/lung_data/Lung-10X_P7_8/genes.tsv → monocle/lung_data/Lung-10X_P7_8/genes.tsv
diff --git a/lung_data/Lung-10X_P7_8/matrix.mtx → monocle/lung_data/Lung-10X_P7_8/matrix.mtx b/lung_data/Lung-10X_P7_8/matrix.mtx → monocle/lung_data/Lung-10X_P7_8/matrix.mtx
diff --git a/..._data/Lung-10X_P7_8/mmLung_classifier.RDS → ..._data/Lung-10X_P7_8/mmLung_classifier.RDS b/..._data/Lung-10X_P7_8/mmLung_classifier.RDS → ..._data/Lung-10X_P7_8/mmLung_classifier.RDS
diff --git a/lung_data/Lung-10X_P7_8/mmLung_markers.txt → ...ung_data/Lung-10X_P7_8/mmLung_markers.txt b/lung_data/Lung-10X_P7_8/mmLung_markers.txt → ...ung_data/Lung-10X_P7_8/mmLung_markers.txt
diff --git a/lung_data/Lung-10X_P7_8/readme → monocle/lung_data/Lung-10X_P7_8/readme b/lung_data/Lung-10X_P7_8/readme → monocle/lung_data/Lung-10X_P7_8/readme
diff --git a/lung_data/readme → monocle/lung_data/readme b/lung_data/readme → monocle/lung_data/readme
diff --git a/monocle.md → monocle/monocle.md b/monocle.md → monocle/monocle.md
diff --git a/scRNAseq_class1_make_CDS.md → monocle/scRNAseq_class1_make_CDS.md b/scRNAseq_class1_make_CDS.md → monocle/scRNAseq_class1_make_CDS.md
diff --git a/scRNAseq_class2_markdown.md → monocle/scRNAseq_class2_markdown.md b/scRNAseq_class2_markdown.md → monocle/scRNAseq_class2_markdown.md
diff --git a/scRNAseq_class2_preprocess_UMAP.Rmd → monocle/scRNAseq_class2_preprocess_UMAP.Rmd b/scRNAseq_class2_preprocess_UMAP.Rmd → monocle/scRNAseq_class2_preprocess_UMAP.Rmd
diff --git a/scRNAseq_class3_Garnett.md → monocle/scRNAseq_class3_Garnett.md b/scRNAseq_class3_Garnett.md → monocle/scRNAseq_class3_Garnett.md
diff --git a/scRNAseq_class4_markdown.md → monocle/scRNAseq_class4_markdown.md b/scRNAseq_class4_markdown.md → monocle/scRNAseq_class4_markdown.md
diff --git a/scRNAseq_class4_pseudotime_DEG.Rmd → monocle/scRNAseq_class4_pseudotime_DEG.Rmd b/scRNAseq_class4_pseudotime_DEG.Rmd → monocle/scRNAseq_class4_pseudotime_DEG.Rmd
diff --git a/solutions/week1_solutions.txt b/solutions/week1_solutions.txt
diff --git a/solutions/week2_solutions.txt b/solutions/week2_solutions.txt
diff --git a/solutions/week3_solutions.txt b/solutions/week3_solutions.txt
diff --git a/solutions/week4_solutions.txt b/solutions/week4_solutions.txt
diff --git a/week1.txt b/week1.txt
diff --git a/week2.txt b/week2.txt
diff --git a/week3.txt b/week3.txt
diff --git a/week4.txt b/week4.txt